Skip to main content
Log in

Running spell-check to identify regulatory variants

  • News & Views
  • Published:

From Nature Genetics

View current issue Submit your manuscript

A major challenge in human genetics is pinpointing which non-coding genetic variants affect gene expression and disease risk. A new study in this issue describes a broadly applicable approach for this task that explicitly models cell type–specific regulatory motifs and generates variant effect predictions that are more accurate and interpretable than those of alternative tools.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Figure 1: Correlation of conservation measures and functional effects with gene expression.

References

  1. Cooper, G.M. & Shendure, J. Nat. Rev. Genet. 12, 628–640 (2011).

    Article  CAS  Google Scholar 

  2. Trynka, G. et al. Nat. Genet. 45, 124–130 (2013).

    Article  CAS  Google Scholar 

  3. Lee, D. et al. Nat. Genet. 47, 955–961 (2015).

    Article  CAS  Google Scholar 

  4. Villar, D. et al. Cell 160, 554–566 (2015).

    Article  CAS  Google Scholar 

  5. Fu, Y. et al. Genome Biol. 15, 480 (2014).

    Article  Google Scholar 

  6. Kircher, M. et al. Nat. Genet. 46, 310–315 (2014).

    Article  CAS  Google Scholar 

  7. Ritchie, G.R., Dunham, I., Zeggini, E. & Flicek, P. Nat. Methods 11, 294–296 (2014).

    Article  CAS  Google Scholar 

  8. Gulko, B., Hubisz, M.J., Gronau, I. & Siepel, A. Nat. Genet. 47, 276–283 (2015).

    Article  CAS  Google Scholar 

  9. Ghandi, M., Lee, D., Mohammad-Noori, M. & Beer, M.A. PLoS Comput. Biol. 10, e1003711 (2014).

    Article  Google Scholar 

  10. Patwardhan, R.P. et al. Nat. Biotechnol. 30, 265–270 (2012).

    Article  CAS  Google Scholar 

  11. Gusev, A. et al. Am. J. Hum. Genet. 95, 535–552 (2014).

    Article  CAS  Google Scholar 

  12. Ma, W. et al. Nat. Methods 12, 71–78 (2015).

    Article  Google Scholar 

  13. Davydov, E.V. et al. PLoS Comput. Biol. 6, e1001025 (2010).

    Article  Google Scholar 

  14. Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R. & Siepel, A. Genome Res. 20, 110–121 (2010).

    Article  CAS  Google Scholar 

  15. Siepel, A. et al. Genome Res. 15, 1034–1050 (2005).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jay Shendure.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kircher, M., Shendure, J. Running spell-check to identify regulatory variants. Nat Genet 47, 853–855 (2015). https://doi.org/10.1038/ng.3364

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.3364

  • Springer Nature America, Inc.

Navigation